Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
Trl

Cell type

Cell type Class
Cell line
Cell type
S2
Source
Oregon R
Developmental Stage
late embryonic stage

Attributes by original data submitter

Sample

source_name
S2_GAFRNAi_GAFChIP
cell line
S2
genotype/variation
GAFRNAi
chip anitbody
Anti-GAF (affinity purified, lab made)

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Cells were washed with ice cold PBS, then fixed in 1% Formaldehyde in PBS at 25 °C for 10 min. Formaldehyde was quenched with 0.125 M glycine. Anti-GAF (affinity purified, lab made) was coupled to Sheep-Anti-Rabbit M280 dynabeads (1:200 concentration). IPs were performed overnight at 4 °C, and after washing beads, crosslinks were reversed using SDS and Proteinase K overnight at 65 °C. Libraries were constructed using the NEB Next Ultra II DNA library prep kit.

Sequencing Platform

instrument_model
NextSeq 500

dm6

Number of total reads
22968059
Reads aligned (%)
90.3
Duplicates removed (%)
10.6
Number of peaks
6448 (qval < 1E-05)

dm3

Number of total reads
22968059
Reads aligned (%)
90.7
Duplicates removed (%)
10.0
Number of peaks
7473 (qval < 1E-05)

Base call quality data from DBCLS SRA